KDM4B p.Lys47=
c.141G>A · VCV3369017
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.82 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.68 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 22.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- KDM4B
- Protein
- p.Lys47=
- Coding
- c.141G>A
- MANE Select
- NM_015015
- Type
- single nucleotide variant
- Location
- chr19:5033031 (GRCh38)
- Gene constraint
- LOEUF 0.371 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.50 · 6 PDB
- Residue 47
- the jmjn domain; a β-strand
Similar variants
- KDM4B c.432+1G>A Pathogenic/Likely pathogenic ★★ same type
- KDM4B p.His768Arg Likely pathogenic ★★ same type
- KDM4B p.Ala187Thr Uncertain significance ★★ ⚠ same type
- KDM4B p.Ala651Asp Uncertain significance ★★ ⚠ same type
- KDM4B p.Ala706Gly Uncertain significance ★★ ⚠ same type
- KDM4B p.Ala759Thr Uncertain significance ★★ ⚠ same type
- KDM4B p.Arg1020His Uncertain significance ★★ ⚠ same type
- KDM4B p.Arg1035Cys Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/kdm4b-p-lys47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown